Currently, Shopify doesn't allow us to deactivate their order confirmation email, so to prevent the customer from receiving two receipts, we recommend that you replace the order confirmation with a simple "thank you" message.
Create Your Template
We’ve made it easy for you to quickly design a new “thank you” note and add it to Shopify. Just go to Notification Templates in Conversio and start designing!
Once you're happy with your template, click the “Get Code” button to copy the HTML.
Replace Order Confirmation
Next, log in to your Shopify store and go to your Settings page.
Select Notifications from the Settings menu.
Select the order confirmation template.
Select the HTML email tab.
Then copy and paste the HTML from the previous step into this area. Click save and voila! :)